GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization

Abstract

Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates in 2018). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/ genomegraphr/).